[mira_talk] Getting observed insert size etc for paired end reads
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 12 Feb 2014 18:15:14 +0000
Hi Bastien,
For paired end libraries, does MIRA report any of the observed
template/insert size, orientation, fraction assembled in same
contig, or something like the SAM FLAG for "properly mapped"
somewhere?
I've been running a few paired end assemblies and not telling
MIRA the expected template size (because I don't know it, or
don't trust the reported figure, or I'm lazy), and was looking
for a quick way to get the apparent distribution post-assembly.
I can see how to extract this from the MAF or SAM file, but
is there a shortcut I'm missing?
Thanks,
Peter
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